Jonathan D.

Mahoney
Storrs, CT
(515).979.0872
jonathan.mahoney@uconn.edu
jonmahoney.weebly.com

Research Interests
Plant Breeding | Plant Physiology | Plant Tissue Culture | Computational Biology | Applied Statistics

Qualifications
• Over 5 years of applied plant science training in plant tissue culture, plant breeding, plant
physiology and functional genomics.
• Knowledge of experimental design in laboratory and field settings, statistical data analysis using
R and communication of scientific results.
• Proficient in conducting plant breeding and plant physiology experiments, utilizing computational
resources and interpreting scientific results.
• Experience in transitioning new scientific discoveries from the lab to the marketplace.

Education
University of Connecticut, Storrs, Connecticut 2020 expected
Department of Plant Sciences and Landscape Architecture
Ph.D. Candidate, Plant Breeding & Horticulture
Dissertation title: Genetic improvement and functional genomics of Aronia
Iowa State University, Ames, Iowa 2014
Department of Horticulture
B.Sc., Horticulture

Professional Experience
Graduate Research Assistant 2015-present
University of Connecticut, Dept. of Plant Science; Storrs, CT
Advisor: Dr. Mark Brand
Committee Members: Dr. Huanzhong Wang, Dr. Yi Li, Dr. Kent Holsinger
• Breeding improved Aronia via intergeneric hybridization and sexual polyploidization for the
commercial fruit and ornamental industries.
• Investigating the mating systems and compatibility between intergeneric hybrids to provide
direction for future breeding efforts and to reveal the symptoms of hybrid necrosis.
• Genotyping wild and cultivated Aronia, Berberis (barberry) and Cannabis germplasm to
determine genetic relatedness, population structure, hybridization and inbreeding.
• Phenotyping Aronia germplasm for fruit biochemical, chill unit requirements and leaf
morphology traits to help guide future breeding efforts.
• Performing computational biology and transcriptomics to identify genes involved with
polyphenol biosynthesis in Aronia fruit.
• Developing tissue culture methods for Aronia shoot organogenesis, micrografting, embryo rescue
and gene transformation.
 Jonathan D. Mahoney 2

Service-learning Intern 2014

Iowa State University, Dept. of Horticulture; St. John, USVI
Advisor: Dr. Dave Minner
• Established an integrated hands-on curriculum for horticulture and plant genetics at Gifft Hill
School on St. John, USVI.
• Developed and presented lessons on plant biology and plant breeding to K-12 students.
• Conducted evaluations on vegetable germplasm for tropical regions to improve sustainable food
production at Gifft Hill School.
• Assisted with producing healthy and locally grown food for the St. John community.

Biological Science Intern 2012-2014

USDA-ARS, NCRPIS; Ames, IA
Advisors: Dr. Candice Gardner and Jeffrey Carstens
• Conserved woody-ornamental germplasm and associated information to support researchers and
breeding programs.
• Implemented novel and efficient methods for phenotyping germplasm collections to improve
available data for researchers.
• Improved seed viability testing methods for woody-ornamental taxa to support efforts of long-
term storage of germplasm.
• Studied the effect of cold-stratification seed treatments on Aronia spp. with the goal of improving
germination rates.
• Provided technical assistance to curator with plant propagation, field establishment, data
collection, harvesting and seed cleaning.

Summer Scholar 2013

Cornell University, Dept. of Horticulture; Geneva, NY
Advisor: Dr. Larry Smart
• Developed and implemented a research project to assist with the genetic improvement of fast-
growing willow shrub (Salix spp.) as a bioenergy crop.
• Conducted research on Salix spp. genotypes for insect pest resistance through choice and no-
choice feeding bioassays and field observations.
• Developed a rating scale for field observations to determine an accurate percentage of leaf
defoliation caused by imported willow leaf beetle (Plagiodera versicolora).

Skills
Computer Proficiency: R [statistics, genetic analysis, bioinformatics, data visualization], SAS, Unix,
running jobs on computing cluster, GeneMarker, I4A, STRUCTURE.
Lab: DNA/RNA extraction, PCR/qRT-PCR, flow cytometry, ploidy manipulation, chemical
mutagenesis, fruit biochemical analyses [pH differential, Folin-Cicalteu, Brix, TA], microscopy,
managing lab safety procedures and inspections, overseeing lab inventory.
Tissue Culture: Micropropagation, shoot organogenesis, gene transformation, genome editing, embryo
rescue, micro-grafting.
Greenhouse/Field: Propagation, grafting, plant maintenance, plant trials, data collection.
Other: Experimental design and statistical data analysis, managing undergraduate and visiting
researchers, working independently.
 Jonathan D. Mahoney 3

Teaching Assistant
University of Connecticut
Woody Plants: Common Trees, Shrubs and Vines – Fall ’15, ‘16
Plant Propagation – Spring ’15, ’16, ’17, ‘18
Plant Tissue Culture – Fall ’17, ‘19

Recent Honors
UConn National Science Foundation Innovation Corps participant 2019
UConn Plant Science Koch Travel Award – Plant & Animal Genome Conference 2019
New York Academy of Sciences STEM Exchange: Research and Career Program 2018
American Society for Horticultural Science Conference Travel Award 2018
UConn Plant Science Koch Travel Award – ASHS Conference 2018
Clifford R. Burr Scholarship 2017
Proven Winners Innovations in Plant Breeding Scholarship 2016
Outstanding Poster Presentation – 2016 CAHNR Graduate Forum 2016
Deland Award – The Arnold Arboretum of Harvard University 2015

Leadership
University of Connecticut – Science of GMOs; Team member 2019-present
University of Connecticut Graduate Student Senate; Senator 2016
University of Connecticut – CAHNR Graduate Student Council; Representative, 2017
PLANTalks; Treasurer 2016-2018
Alpha Zeta; Bylaws Committee 2014
Pi Alpha Xi; Secretary 2013
ISU Horticulture Club; Treasurer & Fall Festival Chairman 2012

Professional Societies
American Society for Horticultural Science
American Society of Plant Biologists
International Plant Propagators Society

Refereed Publications
Kurtz LE, Mahoney JD, Brand MH, Lubell-Brand JD. 2020. Comparing Genotypic and
Phenotypic Variation of Selfed and Outcrossed Progeny of Hemp. HortScience in press
Mahoney JD, Hau T, Connolly BA, Brand MH. 2019. Mixed reproductive strategies in the genus
Aronia: sexual diploids, apomictic tetraploids, and varied triploids. HortScience 54:642-646
Mahoney JD, Apicella PV, Brand MH. 2018. Adventitious Shoot Regeneration from in vitro
Leaves of Aronia mitschurinii and Cotyledons of Closely Related Pyrinae Taxa. Sci Hortic (Amst)
237:135-141

Publications In Prep
Mahoney JD, Iorio LA, Wegrzyn JL, Dorris M, Martin D, Bolling BW, Brand MH, Wang H.
2020. De novo assembly of Aronia melanocarpa fruit transcriptome to identify genes involved with
anthocyanin biosynthesis.
Mahoney JD, Ristvey AG, Brand MH. 2020. Chilling accumulation requirements for black
fruited Aronia species.
Zhang CJ, Mahoney JD, Kim DS, Sun S, Gan L, Yan X. 2020. Pollen longevity, flowering
phenology, and seedbank persistence of Camelina sativa and congenic species.
 Jonathan D. Mahoney 4

Research Presentations
Oral Presentations
Mahoney J. “Unraveling the genetics of polyphenol biosynthesis in Aronia fruit using de novo
RNA sequencing”, CAHNR Graduate Research Forum. Storrs, Connecticut. April 2019.
Mahoney J. “Aronia breeding at the University of Connecticut”, Midwest Aronia Association.
Des Moines, Iowa. March 2019.
Mahoney J. “A Meiotic Mistake Yields Massive Gains: Breeding Improved Aronia via Sexual
Polyploidization”, CAHNR Graduate Research Forum. Storrs, Connecticut. March 2017.
Mahoney J. “Breeding improved Aronia for the commercial fruit industry”, PSLA Graduate
Student Seminar. Storrs, Connecticut. March 2016.
Mahoney J. “Breeding the next generation of anthocyanin-rich pome fruits”, International
Graduate Student Academic Conference. Nanjing, China. October 2015
Mahoney J. “From Seed to Seed: Curating Horticultural Crop Germplasm”, USDA-ARS, TARS.
Mayaguez, Puerto Rico. November 2014.
Poster Presentations
Mahoney J., Iorio L., Wegrzyn J., Dorris M., Martin D., Bolling B., Brand M. and Wang H. “De
novo assembly of Aronia melanocarpa fruit transcriptome to identify genes involved with anthocyanin
biosynthesis”, Plant & Animal Genome Conference. San Diego, California. January 2020.
Mahoney J., Iorio L., Wegrzyn J., Dorris M., Martin D., Bolling B., Brand M. and Wang H.
“Transcriptome analysis of Aronia melanocarpa fruit identifies genes involved in polyphenol
biosynthesis”, Plant & Animal Genome Conference. San Diego, California. January 2019.
Mahoney J., Apicella P., Gardner J., Iorio L., Wang H. and Brand M. “Aronia Breeding: The
next generation of antioxidant-rich pome fruits”, New York Academy of Sciences and Pepsi Co. STEM
Exchange. New York, New York. August 2018.
Mahoney J., Hau T., Brand M. “Apomictic and Sexual Seed Reproduction in Aronia and
Implications for Breeding and Commercial Fruit Cultivars”, American Society for Horticultural Science
Annual Conference. Washington, D.C. July 2018.
Iorio L., Mahoney J., Brand M., Wang H. “Functional genomics of Aronia fruit polyphenol
biosynthesis”, American Society of Plant Biologist, Northeast Section. Amherst, Massachusetts. April
2018.
Mahoney J., Hau T., Brand M. “Sexual and apomictic reproduction in Aronia species and lack of
genetic diversity in commercial Aronia production”, American Society of Plant Biologist, Northeast
Section. Amherst, Massachusetts. April 2018.
Mahoney J., Brand M. “Adventitious Shoot Regeneration from in vitro Leaves of Aronia ×
mitschurinii and Cotyledons of Closely Related Pyrinae Taxa”, American Society of Plant Biologist,
Northeast Section. New Haven, Connecticut. April 2017.
Mahoney J., Brand M. “Organogenic response among closely related Pyrinae taxa”, CAHNR
Graduate Research Forum. Storrs, Connecticut. March 2016.
Mahoney J., Balestri F., Graves W. “Iowa State University Heritage Tree Program: preserving
the genetic heritage of Iowa State’s award-winning campus”, American Society for Horticultural Science
Annual Conference. Orlando, Florida. July 2014.
Mahoney J., Gouker F., Smart L. “Assessment of shrub willow (Salix spp.) genotypes for insect
pest resistance through feeding bioassays and field observations”, Cornell Summer Scholars Presentation
Series. Geneva, New York. July 2013.

Extension Outreach Presentations

Oral Presentations
Mahoney J. “Genetic Modification: The Science and Issues”, New England Vegetable & Berry
Growers’ Association Meeting – Hudson, Massachusetts. February 2020.
Mahoney J. “Playing with genes: Plant breeding and biotechnology”, 4-H Adventures in STEM
– University of Connecticut. Storrs, Connecticut. November 2019.
 Jonathan D. Mahoney 5

Mahoney J. “Plant tissue culture and biotechnology”, Naugatuck Valley Community College
students – University of Connecticut. Storrs, Connecticut. October 2019.
Mahoney J. “Breeding the Next Generation of Antioxidant-rich Pome Fruits: Intergeneric
Hybridization”, Arnold Arboretum of Harvard University. Boston, Massachusetts. May 2017.
Mahoney J. “Aronia: Diversifying Agricultural Production in the Midwest”, Iowa State Fair. Des
Moines, Iowa. June 2015.
Mahoney J. “Mixing it up in the Rosaceae”, Arnold Arboretum of Harvard University. Boston,
Massachusetts. June 2015.
Mahoney J. “USDA, ARS-NCRPIS Woody-ornamental curation: mission and objectives”,
Annual Genebank Managers Meeting. Ames, Iowa. September 2013
Mahoney J., Smith. N., Dvorak. C., Walters. K. “Sycamore Row: history, physiology, proper
documentation, and long-term evaluation”, Department of Horticulture Seminar. Ames, Iowa. March
2013.

Germplasm Collection Trips

Carstens J., Bevins M., Mahoney J., Balestri F. Iowa. Collection of native Betula nigra and
documentation of associated information. June 2014 (Two days).
Carstens J., Mahoney J. Illinois, Indiana, Ohio, and Michigan. Identification and collection of
native Fraxinus quadrangulata populations. August 2013 (Four days).
Carstens J., Mahoney J. Iowa, Illinois, and Indiana. Identification and collection of native
Fraxinus quadrangulata populations. July 2012 (Eight days).
Carstens J., Mahoney J. Iowa. Identification and collection of native Phlox pilosa. July 2012
(One day).

References
Dr. Mark Brand: Major professor
Professor of Horticulture; University of Connecticut – Dept. of Plant Science
1390 Storrs Road - Unit 4163
Storrs, CT 06269
860-486-2930 mark.brand@uconn.edu

Dr. Huanzhong Wang: Committee member / co-PI

Associate Professor; University of Connecticut – Dept. of Plant Science
1390 Storrs Road - Unit 4163
Storrs, CT 06269
860-486-4443 huanzhong.wang@uconn.edu

Jeffrey Carstens: USDA supervisor | collaborator

Woody-ornamental Curator; USDA-ARS Plant Introduction Station
G212 Agronomy Hall
Iowa State University
Ames, Iowa 50011-1170
515-294-3454 Jeffrey.Carstens@ars.usda.gov